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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:ALK-SCEL

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ALK-SCEL
FusionPDB ID: 4080
FusionGDB2.0 ID: 4080
HgeneTgene
Gene symbol

ALK

SCEL

Gene ID

238

8796

Gene nameALK receptor tyrosine kinasesciellin
SynonymsCD246|NBLST3-
Cytomap

2p23.2-p23.1

13q22.3

Type of geneprotein-codingprotein-coding
DescriptionALK tyrosine kinase receptorCD246 antigenanaplastic lymphoma receptor tyrosine kinasemutant anaplastic lymphoma kinasesciellin
Modification date2020032920200313
UniProtAcc

Q96BT7

.
Ensembl transtripts involved in fusion geneENST idsENST00000389048, ENST00000431873, 
ENST00000498037, 		ENST00000469982, 
ENST00000349847, ENST00000377246, 
ENST00000535157, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 13 X 4=5207 X 7 X 5=245
# samples 108
** MAII scorelog2(10/520*10)=-2.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/245*10)=-1.61470984411521
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: ALK [Title/Abstract] AND SCEL [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ALK(29754781)-SCEL(78202082), # samples:3
Anticipated loss of major functional domain due to fusion event.ALK-SCEL seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ALK-SCEL seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
ALK-SCEL seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
ALK-SCEL seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneALK

GO:0016310

phosphorylation

9174053

HgeneALK

GO:0046777

protein autophosphorylation

9174053

TgeneSCEL

GO:0030216

keratinocyte differentiation

14632196


check buttonFusion gene breakpoints across ALK (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across SCEL (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4UCECTCGA-EO-A3AS-01AALKchr2

29754781

-SCELchr13

78202082

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000389048ALKchr229754781-ENST00000535157SCELchr1378202082+348520619072499530
ENST00000389048ALKchr229754781-ENST00000377246SCELchr1378202082+348920619072499530
ENST00000389048ALKchr229754781-ENST00000349847SCELchr1378202082+273520619072499530

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000389048ENST00000535157ALKchr229754781-SCELchr1378202082+0.0243948160.97560513
ENST00000389048ENST00000377246ALKchr229754781-SCELchr1378202082+0.0244656610.9755343
ENST00000389048ENST00000349847ALKchr229754781-SCELchr1378202082+0.0688683240.93113166

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>4080_4080_1_ALK-SCEL_ALK_chr2_29754781_ENST00000389048_SCEL_chr13_78202082_ENST00000349847_length(amino acids)=530AA_BP=385
MGAIGLLWLLPLLLSTAAVGSGMGTGQRAGSPAAGPPLQPREPLSYSRLQRKSLAVDFVVPSLFRVYARDLLLPPSSSELKAGRPEARGS
LALDCAPLLRLLGPAPGVSWTAGSPAPAEARTLSRVLKGGSVRKLRRAKQLVLELGEEAILEGCVGPPGEAAVGLLQFNLSELFSWWIRQ
GEGRLRIRLMPEKKASEVGREGRLSAAIRASQPRLLFQIFGTGHSSLESPTNMPSPSPDYFTWNLTWIMKDSFPFLSHRSRYGLECSFDF
PCELEYSPPLHDLRNQSWSWRRIPSEEASQMDLLDGPGAERSKEMPRGSFLLLNTSADSKHTILSPWMRSSSEHCTLAVSVHRHLQPSGR
YIAQLLPHNEAAREILLMPTPGKHGDQNLENLIEVNSHVSENKNGSSNTGAKQAGPQDTVVYTRTYVENSKSPKDGYQENISGKYIQTVY

--------------------------------------------------------------

>4080_4080_2_ALK-SCEL_ALK_chr2_29754781_ENST00000389048_SCEL_chr13_78202082_ENST00000377246_length(amino acids)=530AA_BP=385
MGAIGLLWLLPLLLSTAAVGSGMGTGQRAGSPAAGPPLQPREPLSYSRLQRKSLAVDFVVPSLFRVYARDLLLPPSSSELKAGRPEARGS
LALDCAPLLRLLGPAPGVSWTAGSPAPAEARTLSRVLKGGSVRKLRRAKQLVLELGEEAILEGCVGPPGEAAVGLLQFNLSELFSWWIRQ
GEGRLRIRLMPEKKASEVGREGRLSAAIRASQPRLLFQIFGTGHSSLESPTNMPSPSPDYFTWNLTWIMKDSFPFLSHRSRYGLECSFDF
PCELEYSPPLHDLRNQSWSWRRIPSEEASQMDLLDGPGAERSKEMPRGSFLLLNTSADSKHTILSPWMRSSSEHCTLAVSVHRHLQPSGR
YIAQLLPHNEAAREILLMPTPGKHGDQNLENLIEVNSHVSENKNGSSNTGAKQAGPQDTVVYTRTYVENSKSPKDGYQENISGKYIQTVY

--------------------------------------------------------------

>4080_4080_3_ALK-SCEL_ALK_chr2_29754781_ENST00000389048_SCEL_chr13_78202082_ENST00000535157_length(amino acids)=530AA_BP=385
MGAIGLLWLLPLLLSTAAVGSGMGTGQRAGSPAAGPPLQPREPLSYSRLQRKSLAVDFVVPSLFRVYARDLLLPPSSSELKAGRPEARGS
LALDCAPLLRLLGPAPGVSWTAGSPAPAEARTLSRVLKGGSVRKLRRAKQLVLELGEEAILEGCVGPPGEAAVGLLQFNLSELFSWWIRQ
GEGRLRIRLMPEKKASEVGREGRLSAAIRASQPRLLFQIFGTGHSSLESPTNMPSPSPDYFTWNLTWIMKDSFPFLSHRSRYGLECSFDF
PCELEYSPPLHDLRNQSWSWRRIPSEEASQMDLLDGPGAERSKEMPRGSFLLLNTSADSKHTILSPWMRSSSEHCTLAVSVHRHLQPSGR
YIAQLLPHNEAAREILLMPTPGKHGDQNLENLIEVNSHVSENKNGSSNTGAKQAGPQDTVVYTRTYVENSKSPKDGYQENISGKYIQTVY

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Fusion Protein Functional Features


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:29754781/chr13:78202082)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
ALK

Q96BT7

.
FUNCTION: Catalyzes the methylation of 5-carboxymethyl uridine to 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in tRNA via its methyltransferase domain (PubMed:20123966, PubMed:20308323, PubMed:31079898). Catalyzes the last step in the formation of 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in target tRNA (PubMed:20123966, PubMed:20308323). Has a preference for tRNA(Arg) and tRNA(Glu), and does not bind tRNA(Lys)(PubMed:20308323). Binds tRNA and catalyzes the iron and alpha-ketoglutarate dependent hydroxylation of 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in tRNA via its dioxygenase domain, giving rise to 5-(S)-methoxycarbonylhydroxymethyluridine; has a preference for tRNA(Gly) (PubMed:21285950). Required for normal survival after DNA damage (PubMed:20308323). May inhibit apoptosis and promote cell survival and angiogenesis (PubMed:19293182). {ECO:0000269|PubMed:19293182, ECO:0000269|PubMed:20123966, ECO:0000269|PubMed:20308323, ECO:0000269|PubMed:21285950, ECO:0000269|PubMed:31079898}.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633619_685542.6666666666666689.0DomainLIM zinc-binding
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532619_685522.6666666666666669.0DomainLIM zinc-binding
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431619_685500.6666666666667647.0DomainLIM zinc-binding
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633544_563542.6666666666666689.0RepeatNote=16
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532524_543522.6666666666666669.0RepeatNote=15
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532544_563522.6666666666666669.0RepeatNote=16
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431505_523500.6666666666667647.0RepeatNote=14
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431524_543500.6666666666667647.0RepeatNote=15
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431544_563500.6666666666667647.0RepeatNote=16

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneALKchr2:29754781chr13:78202082ENST00000389048-429816_940384.66666666666671621.0Compositional biasNote=Gly-rich
HgeneALKchr2:29754781chr13:78202082ENST00000389048-4291116_1392384.66666666666671621.0DomainProtein kinase
HgeneALKchr2:29754781chr13:78202082ENST00000389048-429264_427384.66666666666671621.0DomainMAM 1
HgeneALKchr2:29754781chr13:78202082ENST00000389048-429437_473384.66666666666671621.0DomainNote=LDL-receptor class A
HgeneALKchr2:29754781chr13:78202082ENST00000389048-429478_636384.66666666666671621.0DomainMAM 2
HgeneALKchr2:29754781chr13:78202082ENST00000389048-4291197_1199384.66666666666671621.0RegionNote=Inhibitor binding
HgeneALKchr2:29754781chr13:78202082ENST00000389048-4291060_1620384.66666666666671621.0Topological domainCytoplasmic
HgeneALKchr2:29754781chr13:78202082ENST00000389048-42919_1038384.66666666666671621.0Topological domainExtracellular
HgeneALKchr2:29754781chr13:78202082ENST00000389048-4291039_1059384.66666666666671621.0TransmembraneHelical
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633251_563542.6666666666666689.0RegionNote=16 X approximate tandem repeats
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532251_563522.6666666666666669.0RegionNote=16 X approximate tandem repeats
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431251_563500.6666666666667647.0RegionNote=16 X approximate tandem repeats
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633251_266542.6666666666666689.0RepeatNote=1
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633267_286542.6666666666666689.0RepeatNote=2
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633287_306542.6666666666666689.0RepeatNote=3
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633307_326542.6666666666666689.0RepeatNote=4
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633327_346542.6666666666666689.0RepeatNote=5
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633347_366542.6666666666666689.0RepeatNote=6
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633387_406542.6666666666666689.0RepeatNote=8
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633407_426542.6666666666666689.0RepeatNote=9
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633427_446542.6666666666666689.0RepeatNote=10
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633447_465542.6666666666666689.0RepeatNote=11
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633466_484542.6666666666666689.0RepeatNote=12
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633485_504542.6666666666666689.0RepeatNote=13
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633505_523542.6666666666666689.0RepeatNote=14
TgeneSCELchr2:29754781chr13:78202082ENST000003498472633524_543542.6666666666666689.0RepeatNote=15
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532251_266522.6666666666666669.0RepeatNote=1
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532267_286522.6666666666666669.0RepeatNote=2
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532287_306522.6666666666666669.0RepeatNote=3
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532307_326522.6666666666666669.0RepeatNote=4
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532327_346522.6666666666666669.0RepeatNote=5
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532347_366522.6666666666666669.0RepeatNote=6
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532387_406522.6666666666666669.0RepeatNote=8
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532407_426522.6666666666666669.0RepeatNote=9
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532427_446522.6666666666666669.0RepeatNote=10
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532447_465522.6666666666666669.0RepeatNote=11
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532466_484522.6666666666666669.0RepeatNote=12
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532485_504522.6666666666666669.0RepeatNote=13
TgeneSCELchr2:29754781chr13:78202082ENST000003772462532505_523522.6666666666666669.0RepeatNote=14
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431251_266500.6666666666667647.0RepeatNote=1
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431267_286500.6666666666667647.0RepeatNote=2
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431287_306500.6666666666667647.0RepeatNote=3
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431307_326500.6666666666667647.0RepeatNote=4
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431327_346500.6666666666667647.0RepeatNote=5
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431347_366500.6666666666667647.0RepeatNote=6
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431387_406500.6666666666667647.0RepeatNote=8
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431407_426500.6666666666667647.0RepeatNote=9
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431427_446500.6666666666667647.0RepeatNote=10
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431447_465500.6666666666667647.0RepeatNote=11
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431466_484500.6666666666667647.0RepeatNote=12
TgeneSCELchr2:29754781chr13:78202082ENST000005351572431485_504500.6666666666667647.0RepeatNote=13


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Fusion Protein-Protein Interaction


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
ALKall structure
SCEL


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to ALK-SCEL


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to ALK-SCEL


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneALKC0007131Non-Small Cell Lung Carcinoma28CGI;CTD_human
HgeneALKC0027819Neuroblastoma13CGI;CTD_human;ORPHANET
HgeneALKC0152013Adenocarcinoma of lung (disorder)8CGI;CTD_human
HgeneALKC2751681NEUROBLASTOMA, SUSCEPTIBILITY TO, 38CLINGEN;UNIPROT
HgeneALKC0206180Ki-1+ Anaplastic Large Cell Lymphoma6CGI;CTD_human
HgeneALKC0334121Inflammatory Myofibroblastic Tumor4CGI;CTD_human;ORPHANET
HgeneALKC0018199Granuloma, Plasma Cell3CTD_human
HgeneALKC0007621Neoplastic Cell Transformation2CTD_human
HgeneALKC0027627Neoplasm Metastasis2CTD_human
HgeneALKC0238463Papillary thyroid carcinoma2ORPHANET
HgeneALKC0001973Alcoholic Intoxication, Chronic1PSYGENET
HgeneALKC0006118Brain Neoplasms1CGI;CTD_human
HgeneALKC0006142Malignant neoplasm of breast1CTD_human
HgeneALKC0007134Renal Cell Carcinoma1CTD_human
HgeneALKC0011570Mental Depression1PSYGENET
HgeneALKC0011581Depressive disorder1PSYGENET
HgeneALKC0027643Neoplasm Recurrence, Local1CTD_human
HgeneALKC0036341Schizophrenia1PSYGENET
HgeneALKC0079744Diffuse Large B-Cell Lymphoma1CTD_human
HgeneALKC0085269Plasma Cell Granuloma, Pulmonary1CTD_human
HgeneALKC0153633Malignant neoplasm of brain1CGI;CTD_human
HgeneALKC0278601Inflammatory Breast Carcinoma1CTD_human
HgeneALKC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
HgeneALKC0496899Benign neoplasm of brain, unspecified1CTD_human
HgeneALKC0678222Breast Carcinoma1CTD_human
HgeneALKC0750974Brain Tumor, Primary1CTD_human
HgeneALKC0750977Recurrent Brain Neoplasm1CTD_human
HgeneALKC0750979Primary malignant neoplasm of brain1CTD_human
HgeneALKC1257931Mammary Neoplasms, Human1CTD_human
HgeneALKC1266042Chromophobe Renal Cell Carcinoma1CTD_human
HgeneALKC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
HgeneALKC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
HgeneALKC1306837Papillary Renal Cell Carcinoma1CTD_human
HgeneALKC1332079Anaplastic Large Cell Lymphoma, ALK-Positive1ORPHANET
HgeneALKC1458155Mammary Neoplasms1CTD_human
HgeneALKC1527390Neoplasms, Intracranial1CTD_human
HgeneALKC2931189Neural crest tumor1ORPHANET
HgeneALKC3899155hereditary neuroblastoma1GENOMICS_ENGLAND
HgeneALKC4704874Mammary Carcinoma, Human1CTD_human